Package: TiDEomics
Title: Time-course Differential Expression analysis of omics data
Version: 0.99.7
Date: 2026-10-29
Authors@R: 
    person("Tianen", "He",
            email = "tianen.he@ndm.ox.ac.uk",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6864-0723"))
Description: TiDEomics provides an integrated workflow for multi-group
    time-course omics data analysis. It uses model-based differential
    expression, variance decomposition, and co-expression module analysis
    with WGCNA to characterise temporal, group, and group-specific temporal
    effects. Multi-dataset and multi-omics comparisons and consensus module
    identification can be performed using shared features. The package includes
    quality control, data processing, functional enrichment, and integrated
    visualisation. It supports data with missing values, and
    operates on SummarizedExperiment objects for interoperability with
    the Bioconductor ecosystem.
License: GPL (>= 2)
URL: https://bioconductor.org/packages/TiDEomics/,
        https://github.com/hte123/TiDEomics,
        https://hte123.github.io/TiDEomics
BugReports: https://github.com/hte123/TiDEomics/issues
biocViews: Software, GeneExpression, DifferentialExpression,
        Proteomics, Transcriptomics, TimeCourse, MultipleComparison,
        Pathways, Visualization, QualityControl
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Imports: circlize, clusterProfiler, ComplexHeatmap, dplyr, enrichplot,
        ggforce, ggh4x, ggplot2, ggplotify, ggpubr, ggrepel, ggridges,
        ggsci, limma, lme4, methods, patchwork, pbapply, PCAtools,
        randtests, scales, SummarizedExperiment, tibble, tidyr, Trendy,
        umap, WGCNA
Depends: R (>= 4.6.0)
LazyData: false
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.1.0), plotly,
        enrichR, org.Hs.eg.db, org.Mm.eg.db, msigdbr, DeeDeeExperiment
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.1
git_url: https://git.bioconductor.org/packages/TiDEomics
git_branch: devel
git_last_commit: 8f1ba5a
git_last_commit_date: 2026-10-29
Repository: Bioconductor 3.24
Date/Publication: 2026-10-29
NeedsCompilation: no
Packaged: 2026-10-30 01:50:01 UTC; biocbuild
Author: Tianen He [aut, cre] (ORCID: <https://orcid.org/0000-0001-6864-0723>)
Maintainer: Tianen He <tianen.he@ndm.ox.ac.uk>
